2008

• Coordination Studies of Al-EDTA in Aqueous Solution. Orkid Coskuner, Emily A. A. Jarvis. Journal of Physical Chemistry A 112(12), 2628-2633. (2008)
• Improved Classifier for Computer-aided Polyp Detection in CT Colonography by Nonlinear Dimensionality Reduction. Shijun Wang, Jianhua Yao and Ronald M. Summers. Med. Phys., in press.
• Binding-induced folding of a natively unstructured transcription factor. Turjanski, A. G., Gutkind, J.S., Best, R. and Hummer. G. PLoS Computational Biology, in press.
• Testing logistic regression coefficients with clustered data and few positive outcomes. Sally Hunsberger, Ed Korn, and Barry Graubard. Statistics in Medicine, in press.
• Concentration and crowding effects on protein stability from a coarse-grained model. J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. in Statistical Mechanics of Cellular Systems and Processes, MH Zaman ed, Cambridge Universigty Press, in press.
• Cluster Without Fluster: The Effect of Correlated Outcomes on Inference in Randomized Clinical Trials. Proschan MA, Follmann, DA. Statistics in Medicine, accepted.
• Morphology of Ion Clusters in Aqueous Electrolytes. SA Hassan. Phys. Rev. E 77 (in press).
• 11C-Loperamide and its N-desmethyl radiometabolite are avid substrates for brain P-glycoprotein efflux. Zoghbi SS, Liow J-S, Yasuno F, Hong J, Tuan E; Lazarova N, Gladding RL; Pike VW, Innis RB J. Nucl. Med., in press.
• A pseudopotential for improving the packing of ellipsoidal protein structures determined by NMR. C.D. Schwieters and G.M. Clore. J. Phys. Chem, in press.
• Calcium-dependent inactivation terminates calcium release in skeletal muscle of amphibians. Eduardo Rios, Jingsong Zhou, Gustavo Brum, Bradley S. Launikonis, and Michael D. Stern. J. Gen. Physiol., accepted.
• Coarse Master Equations for Peptide Folding Dynamics. N.V. Buchete and G. Hummer. J. Phys. Chem. B , in press.
• Positron Emission Tomography Imaging Using an Inverse Agonist Radioligand to Assess Cannabinoid CB1 Receptors in Rodents. Terry G, Liow J-S, Chernet E; Zoghbi SS, Phebus L, Felder CC, Tauscher J, Schaus JM, Pike VW, Halldin C, Innis RB. Neuroimage, in press.
• Endogenous retrotransposon sequences of the Schistosoma mansoni intermediate snail host, Biomphalaria glabrata.. Knight M, Bridger J, Ittiprasert W, Odoemelam E, Masabanda J, Miller A, Raghavan, N. In Mobile Genetic Elements in Metazoan Parasites, Brindley PJ (ed). Landes Bioscience, in press.
• Efficient Approximation of P-value of the Maximum of Correlated Tests, with Applications to Genome-Wide Association Studies.. Li Q.Z., Zheng G., Li Z.H. and Yu K. Annals of Human Genetics, in press. (2008).
• A frailty mixture cure model with application to hospital readmission data. Yu, B. Biometrical J., in press (2008).
• Dynamics of Cholesterol Exchange in the OSBP-Related Protein Family. Canagarajah, B., Hummer, G., Prinz, W. and Hurley, J. H. J. Mol. Biol., Published online 4 Feb (2008).
• Privileged scaffolds targeting reverse-turn and helix recognition. Che, Ye & Marshall, Garland. Expert Opinion on Therapeutic Targets, 12(1), 101-114 (2008)
• Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. Rodriguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Aleman C.J Chem Inf Model. 2008 Jan 17 [Epub ahead of print]
• Identification of the Transition States in the Inversion of 1,4-Benzodiazepines with the Ab Initio Replica Path Method. Yong-Sok Lee, Victor W. Pike, and Milan Hodoscek. J. Phys. Chem A, 112, 1604-1611 (2008).
• Genotype, haplotype and copy-number variation in worldwide human populations.. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Nature, 451(7181):998-1003. (2008).
• Dissecting contact potentials for proteins: relative contributions of individual amino acids.. Buchete NV, Straub JE, Thirumalai D. Proteins, 70(1):119-30. (2008).
• Synthesis and evaluation of N-Methyl and S-Methyl 11C-Labeled 6-Methylthio-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridines as radioligands for imaging beta-amyloid plaques in Alzheimer's disease.. Cai L, Liow JS, Zoghbi SS, Cuevas J, Baetas C, Hong J, Shetty HU, Seneca NM, Brown AK, Gladding R, Temme SS, Herman MM, Innis RB, Pike VW. J. Med. Chem., 51(1):148-58 (2008)
• CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. Klauda JB, Brooks BR J. Chem. Theory and Computation, 4(1):107-115. (2008).
• Towards an automatic classification of protein structural domains based on structural similarity. Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics, 9(1):74 (2008).
• New structures help the modeling of toxic amyloid ion channels. Jang H, Zheng J, Lal R, Nussinov R. gTrends Biochem Sci. Feb;33(2):91-100 (2008)
• Sigma Stellation: A Design Strategy for Electron Boxes. Irikura, Karl K J. Phys. Chem A, 112, 983-988. (2008).
• Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study.. Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Zoltick B, Weinberger DR, Meyer-Lindenberg A. Biol. Psychiatry, 63(5):475-83 (2008).

  2007

• Nimbus (BgI): an active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata.. Raghavan N, Tettelin H, Miller A, Hostetler J, Tallon L, Knight M. Int. J. Parasitol., 37(12):1307-18 (2007).
• Neural dynamics for facial threat processing as revealed by gamma band synchronization using MEG. Qian Luo, Tom Holroyd, Matthew Jones, Talma Hendler and James Blair Neuroimage, 34, 839-847 (2007).
• Calibrating E-values for MS2 database search methods. Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Biol. Direct., 2:26 (2007).
• Two-sample Comparison Based on Prediction Error, with Applications to Candidate Gene Association Studies. K. Yu, R. Martin, N. Rothman, T. Zheng, Q. Lan. Annals of Human Genetics, 71 (1) , 107- 118 (2007).
• Protein recognition motifs: Design of peptidomimetics of helix surfaces. Ye Che, Bernard Brooks, Garland R Marshall. Biopolymers, 86(4), 288 - 297 (2007).
• Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2-Ethoxy Tetrahydropyran. H. Lee Woodcock, Damian Moran, Richard W. Pastor, Alexander D. MacKerell, Jr. and Bernard R. Brooks. Biophys. J, 93:1-10 (2007)
• A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release.. Matarin M, Brown WM, Scholz S, Simon-Sanchez J, Fung HC, Hernandez D, Gibbs JR, De Vrieze FW, Crews C, Britton A, Langefeld CD, Brott TG, Brown RD Jr, Worrall BB, Frankel M, Silliman S, Case LD, Singleton A, Hardy JA, Rich SS, Meschia JF. Lancet Neurol., 6(5):414-20. (2007).
• A survey of genetic human cortical gene expression. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nature Genetics, 39(12):1494-9 (2007).
• RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics. Alves G, Ogurtsov AY, Yu YK. Biol. Direct., 2:25 (2007).
• Cysteine-cysteine contact preference leads to target-focusing in protein folding. Sardiu ME, Cheung MS, Yu YK. Biophys. J., 93(3):938-51 (2007).
• Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study. D. Zanuy, F. Rodriguez-Ropero, R. Nussinov, C. Aleman. J. Struct. Biol., 160(2), 177-189 (2007).
• Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn Scaffolds. Y Che, Bernard Brooks, Dennis P Riley, Andrea JH Reaka, Garland R Marshall. Chemical Biology & Drug Design, 69 (2) , 99-110 (2007)
• Challenges in Projecting Clustering Results Across Gene Expression?Profiling Datasets. Lara Lusa, Lisa M. McShane, James F. Reid, Loris De Cecco, Federico Ambrogi, Elia Biganzoli, Manuela Gariboldi, Marco A. Pierotti. J. National Cancer Institute, 99(22), 1715-1723 (2007).
• Natural resonance structures and aromaticity of the nucleobases. Guangyu Sun & Marc Nicklaus. Theoretical Chemistry Accounts: Theory, Computation and Modeling, 117(2), 323-332 (2007).
• The structure of receptor-associated protein (RAP). Donghan Lee Joseph D. Walsh, Molly Migliorini, Ping Yu Tao Cai, Charles D. Schwieters, Susan Krueger, Dudley K. Strickland, and Yun-Xing Wang. Protein Science, 16:1628-1640. (2007).
• Calculation of the Free Energy and Cooperativity of Protein Folding. Alex Kentsis, Tatyana Gindin, Mihaly Mezei, and Roman Osman PLoS ONE, 2(5): e446. (2007).
• Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chio A, Singleton A, Hardy J, Traynor BJ. Lancet Neurol., 6(4):322-8. (2007).
• Effect of a P-glycoprotein inhibitor, Cyclosporin A, on the disposition in rodent brain and blood of the 5-HT1A receptor radioligand, [11C](R)-(-)-RWAY.. Liow JS, Lu S, McCarron JA, Hong J, Musachio JL, Pike VW, Innis RB, Zoghbi SS. Synapse, 61(2):96-105. (2007).
• The Origin of Quantal Size Variation: Vesicular Glutamate Concentration Plays a Significant Role. Xin-Sheng Wu, Lei Xue, Raja Mohan, Kenneth Paradiso, Kevin D. Gillis, and Ling-Gang Wu. J. Neurosc., 27(11):3046-3056 (2007).
• A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences. Joseph C Lee, David Stiles, Jun Lu, and Margaret C Cam. BMC Genomics, 8: 284. (2007).
• Molecular Factors and Biochemical Pathways Induced by Febrile Temperature in Intraerythrocytic Plasmodium falciparum Parasites. Miranda S. M. Oakley, Sanjai Kumar, Vivek Anantharaman, Hong Zheng, Babita Mahajan, J. David Haynes, J. Kathleen Moch Rick Fairhurst Thomas F. McCutchan and L. Aravind. Infection and Immunity, 75, 2012-2025 (2007).
• Models of s-Amyloid Ion Channels in the Membrane Suggest That Channel Formation in the Bilayer Is a Dynamic Process. Hyunbum Jang, Jie Zheng, and Ruth Nussinov. Biophys. J, 93:1938-1949 (2007).
• Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR. Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, Wilce JA. Mol. Cell. Biol., 27(19):6806-17 (2007).
• The bootstrap variance of the square of a sample mean. Dodd, LE and Korn, EL. The American Statistician.. 1 (2): 127-131 (2007)
• Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.. Vogeli B, Ying J, Grishaev A, Bax A. J. Am. Chem. Soc, 129(30):9377-85 (2007).
• Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety.. Ivanov, A. A.; Fricks, I; Harden, T. K.; Jacobson, K. A. Bioorg. Med. Chem. Lett., 17, 761-766. (2007).
• Competition between Hydrogen Abstraction and Halogen Displacement in the Reaction of Br with CH3I, CH3Br, and CH3Cl. Irikura, Karl K.; Francisco, J. S. J. Phys. Chem, 111, 6852-6859. (2007).
• Identification and regional distribution in rat brain of radiometabolites of the dopamine transporter PET radioligand [11C]PE2I.. Shetty HU, Zoghbi SS, Liow JS, Ichise M, Hong J, Musachio JL, Halldin C, Seidel J, Innis RB, Pike VW. Eur. J. Nucl. Med. Mol. Imaging, 34(5):667-78. (2007).
• A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data.. Schwieters CD, Clore GM. Biochemistry, 46(5):1152-66. (2007).
• Preferred conformation of the glycosidic linkage of methyl-beta-mannose.g Coskuner O. J. Chem. Phys, 127(1):015101. (2007).
• Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate.. Ivanov AA, Ko H, Cosyn L, Maddileti S, Besada P, Fricks I, Costanzi S, Harden TK, Calenbergh SV, Jacobson KA. J. Med. Chem, 50(6):1166-76 (2007).
• Analysis of failure time data with multilevel clustering, with application to the child vitamin a intervention trial in Nepal. Shih JH, Lu SE. Biometrics, 63(3):673-80. (2007).
• NIST Computational Chemistry Comparison and Benchmark Database, used by 70,000 distinct hosts in 2007. Some of the calculations in the CCBDB were performed by Russell Johnson on the Biowulf cluster.
• Context-specific amino acid substitution matrices and their use in the detection of protein homologs.. Goonesekere NC, Lee B. Proteins, Nov 2007 (Epub ahead of print).
• Water dissociation in the presence of metal ions.. Coskuner O, Jarvis EA, Allison TC. Angew. Chem. Int. Ed, 46(41), 7853. (2007).
• An investigation of two multivariate permutation methods for controlling the false discovery proportion. Edward L. Korn , Ming-Chung Li , Lisa M. McShane and Richard Simon. Statistics in Medicine, 26:4428-4440 (2007).
• Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution. SA Hassan. J. Phys. Chem B, 111(1):227-41. (2007).
• beta(2)-Microglobulin Amyloid Fragment Organization and Morphology and Its Comparison to Abeta Suggests That Amyloid Aggregation Pathways Are Sequence Specific. Zheng J, Jang H, Nussinov R. Biochemistry. Feb 26;47(8):2497-2509 (2008)
• The LeFE algorithm, embracing the complexity of gene expression in the interpretation of microarray data.. Eichler, GS, Reimers, M, Kane, D, Weinstein, JN. Genome Biology, 8(9):R185 (2007).
• Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures.. Mittal J, Shen VK, Errington JR, Truskett TM. J Chem Phys., Oct 21;127(15):154513. (2007)
• Random Effects Modeling Approaches for Estimating ROC Curves from Repeated Ordinal Tests without a Gold Standard. Paul Albert. Biometrics, 63, 593-602 (2007).
• Comparative Study of the Effect of Tail Corrections on Surface Tension Determined by Molecular Simulation. V. K. Shen, R. D. Mountain, and J. R. Errington. J. Phys. Chem, B 111, 6198 (2007).
• Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions.. J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. Biophys J, 92, 4316 (2007).
• Imputation Approaches for Estimating Diagnostic Accuracy for Multiple Tests from Partially Verified Designs. Paul S. Albert. Biometrics, 63, 947-957 (2007)
• An Evaluation of Power and Type I Error of Single-Nucleotide Polymorphism Transmission/Disequilibrium-Based Statistical Methods under Different Family Structures, Missing Parental Data, and Population Stratification. Kristin K. Nicodemus Augustin Luna and Yin Yao Shugart. Am. J. Hum. Genet., 80, 178-185 (2007).
• Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2. Adina L Milac, Nicolae-Viorel Buchete, Timothy A Fritz, Gerhard Hummer, Lawrence A Tabak J. Mol. Biol., Oct 19;373(2):439-51 (2007)
• Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements. Ma B, Levine AJ. Nucleic Acids Research, accepted.
• Multiple comparisons distortions of parameter estimates. Jeffries, NO. Biostatistics, 8(2):500-4. (2007).
• Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Buchete NV, Hummer G. Biophys J. 2007 May 1;92(9):3032-9. Epub 2007 Feb 9.
• Dissecting contact potentials for proteins: Relative contributions of individual amino acids. Buchete NV, Straub JE, Thirumalai D. Proteins. 2007 Jul 19; [Epub ahead of print]
• Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure.. Klauda JB, Brooks BR. J Mol Biol. 2007 Apr 13;367(5):1523-34
• Probes for Narcotic Receptor Mediated Phenomena. . Hiebel AC, Lee YS, Bilsky E, Giuvelis D, Deschamps JR, Parrish DA, Aceto MD, May EL, Harris LS, Coop A, Dersch CM, Partilla JS, Rothman RB, Cheng K, Jacobson AE, Rice KC. J Med Chem. 2007 Aug 9;50(16):3765-3776..
• Models of {beta}-Amyloid Ion-Channels in the Membrane Suggest that Channel Formation in the Bilayer is a Dynamic Process.. Jang H, Zheng J, Nussinov R. Biophys J. 2007 May 25.
• Modeling the Alzheimer A{beta}17-42 Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities.. Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R. Biophys J. 2007 Aug 3 .
• Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer.. Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Biophys J. 2007 Jul 1;93(1):245-53..
• Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect.. Jang H, Ma B, Nussinov R. BMC Struct Biol. 2007 Apr 2;7:21..
• Use of constrained synthetic amino acids in beta-helix proteins for conformational control.. Zanuy D, Jimenez AI, Cativiela C, Nussinov R, Aleman C. J Phys Chem B. 2007 Mar 29;111(12):3236-42..
• A 2-Year Prospective Study of Human Papillomavirus Persistence among Women with a Cytological Diagnosis of Atypical Squamous Cells of Undetermined Significance or Low-Grade Squamous Intraepithelial LesionPlummer M, Schiffman M, Castle PE, Maucort-Boulch D, Wheeler CM; ALTS Group.J Infect Dis. 2007 Jun 1;195(11):1582-9.
• Calculation of the Free Energy and Cooperativity of Protein FoldingKentsis A, Gindin T, Mezei M, Osman R.PLoS ONE. 2:e446., 2007 May 16
• Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways. Keskin O and Nussinov R.Structure, 15:341-354, 2007 Mar.
• Intrinsic conformational characteristics of alpha,alpha- diphenylglycine. Casanovas J, Zanuy D, Nussinov R, Aleman C.J. Org. Chem., 16;72(6):2174-81, 2007 Mar.
• Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4. Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. J Am Chem Soc., 14;129(6):1602-11, 2007 Feb.

  2006

• Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services Ying He, and Mehmet Kayaalp. AMIA Annu Symp Proc. , 946.(2006).
• Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements.. Ying J, Grishaev A, Bryce DL, Bax A. J. Am. Chem. Soc, 128(35):11443-54. (2006).
• Impact of Cis-proline analogs on peptide conformation. Ye Che, Garland R. Marshall. Biopolymers, 81(5), 392 - 406 (2006).
• Development of small molecules designed to modulate protein-protein interactions. Ye Che, Bernard Brooks, Garland Marshall. J. Computer-Aided Molecular Design, 20(2), 109-130 (2006).
• Engineering Cyclic Tetrapeptides Containing Chimeric Amino Acids as Preferred Reverse-Turn Scaffolds. Ye Che and Garland Marshall. J. Med. Chem., 49 (1), 111 -124, (2006)
• The influence of tumor oxygenation on 18F-FDG (Fluorine-18 Deoxyglucose) uptake: A mouse study using positron emission tomography (PET). Linda W Chan, Sebastien Hapdey, Sean English, Jurgen Seidel, Joann Carson, Anastasia L Sowers, Murali C Krishna, Michael V Green, James B Mitchell and Stephen L Bacharach. Radiation Oncology, 1:3 (2006).
• Automatic colonic polyp detection using multiobjective evolutionary techniques. Jiang Li, Adam Huang, Jianhua Yao, and Ingmar Bitter, Nicholas Petrick, Ronald M. Summers, Perry J. Pickhardt, J. Richard Choi. In Medical Imaging 2006: Image Processing, Joseph M. Reinhardt, Josien P. W. Pluim (eds). (2006).
• A Missense Mutation in the Seven-transmembrane Domain of the Human Ca2+ Receptor Converts a Negative Allosteric Modulator into a Positive Allosteric Modulator. Jianxin Hu, Jiankang Jiang, Stefano Costanzi, Craig Thomas, Wu Yang, Jean H. M. Feyen, Kenneth A. Jacobson, and Allen M. Spiegel. J. Biol. Chem, Vol. 281, Issue 30, 21558-21565 (2006).
• Genes Involved in DNA Repair and Nitrosamine Metabolism and Those Located on Chromosome 14q32 Are Dysregulated in Nasopharyngeal Carcinoma. Lori E. Dodd, Srikumar Sengupta, I-How Chen, Johan A. den Boon, Yu-Juen Cheng, William Westra, Michael A. Newton, Beth F. Mittl, Lisa McShane, Chien-Jen Chen, Paul Ahlquist and Allan Hildesheim. Cancer Epidemiology Biomarkers & Prevention, 15, 2216-2225 (2006).
• Consensus features in amyloid fibrils: sheet?sheet recognition via a (polar or nonpolar) zipper structure. Jie Zheng, Buyong Ma and Ruth Nussinov. Phys. Biol., 3, 1478-3975 (2006).
• Predicting domain-domain interactions using a parsimony approach. Katia S Guimaraes, Raja Jothi, Elena Zotenko and Teresa M Przytycka. Genome Biol., 7(11): R104. (2006).
• Membrane biophysics. Joshua Zimmerberg. Current Biology, 16, R272-R276 (2006).
• De novo peptide sequencing using exhaustive enumeration of peptide composition.. Olson MT, Epstein JA, Yergey AL. J. Am. Soc. Mass. Spectrum 17(8):1041-9 (2006).
• Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins.. Clore GM, Schwieters CD. J. Mol. Biol., 355(5):879-86. (2006).
• PET imaging of the dopamine transporter with 18F-FECNT: a polar radiometabolite confounds brain radioligand measurements.. Zoghbi SS, Shetty HU, Ichise M, Fujita M, Imaizumi M, Liow JS, Shah J, Musachio JL, Pike VW, Innis RB. J. Nucl. Med, 47(3):520-7. (2006).
• ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.. Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics, 7:206. (2006).
• Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose. R. M. Venable, A. Skibinsky and R. W. Pastor. Molecular Simulation, 32, 849-855 (2006).
• Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin.. E L Mehler, S A Hassan, S Kortagere and H Weinstein. Proteins, 64(3):673-90. (2006).
• Augmented designs to assess immune response in vaccine trials.. Follmann, DA. Biometrics, 62(4):1161-9. (2006).
• Effects of electric fields on proton transport through water chains. S A Hassan, G Hummer and Y S Lee J. Chem. Phys, 124, 204510 (2006).
• PET imaging of brain 5-HT1A receptors in rat in vivo with 18F-FCWAY and improvement by successful inhibition of radioligand defluorination with miconazole.. Tipre DN, Zoghbi SS, Liow JS, Green MV, Seidel J, Ichise M, Innis RB, Pike VW. J. Nucl. Med, 47(2):345-53. (2006).
• Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems. L. G. MacDowell, V. K. Shen, and J. R. Errington. J. Chem. Phys, 125, 034705 (2006).
• Nanostructure Design Using Protein Building Blocks Enhanced by Conformationally Constrained Synthetic Residues. Zheng J, Zanuy D, Haspel N, Tsai CJ, Alem C and Nussinov R.Biochemistry, 46(5):1205 -1218, 2007.
• Accounting for Variability in Sample Size Estimation with Applications to Nonadherence and Estimation of Variance and Effect Size. Fay, MP, Halloran, ME, Follmann, DA. Biometrics, Published online: doi: 10.1111/j. 1541-0420.2006.00703.x, 2006 Dec
• Investigation of the catalytic mechanism of farnesyl pyrophosphate synthase by computer simulation. J. Phys. Chem, 110(36):18052-7. (2006)
• Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior.. V. K. Shen, J. K. Cheung, J. R. Errington, and T. M. Truskett. Biophys J, 90, 1949 (2006)
• Determination of surface tension in binary mixtures using transition-matrix Monte Carlo. V. K. Shen and J. R. Errington. J. Chem. Phys, 124, 024721 (2006).
• Dynamical motions of lipids and a finite size effect in simulations of bilayers. . Klauda JB, Brooks BR, Pastor RW. J Chem Phys. 2006 Oct 14;125(14):144710.
• "Similarity Trap” in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 core Domain Complexed with 53BP1 and BRCA1 BRCT Domains. Liu J, Pan Y, Ma B, and Nussinov R.Structure, 14(12):1811-21, 2006 Dec.
• Structural basis for p53 binding-induced DNA bending. Pan Y, Nussinov R., J Biol Chem., 5;282(1):691-9, 2007 Jan.
• Backbone Conformational Preferences and Pseudorotational Ring Puckering of 1-Aminocyclopentane-1-carboxylic Acid. Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 26;110(42):21264-71, 2006 Oct
• Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Jang H, Ma B, Woolf TB, Nussinov R. Biophys J. 15;91(8):2848-59. 2006 Oct.
• Multiple independent evolutionary solutions to core histone gene regulation. Marino-Ramirez L, Jordan IK, Landsman D. Genome Biol. 7(12):R122, 2006.
• Global similarity and local divergence in human and mouse gene co-expression networks.. Tsaparas, P., Marino-Ramirez, L., Bodenreider, O., Koonin, E. V. and Jordan, I. K. BMC Evol Biol.. 6, 70, 2006.
• Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data.. Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Lancet Neurol.. 5, 911-916, 2006.
• The Histone Database: a comprehensive resource for histones and histone fold-containing proteins.. Marino-Ramirez, L., Hsu, B., Baxevanis, A. D. and Landsman, D. Proteins. 62, 838-842, 2006.
• CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome . Sharov A, Dudekula D, Ko MSH. DNA Research. 2006.
• Rat toxicogenomic study reveals analytical consistency across microarray platforms. Guo, L et al. Nature Biotechnology. 24, 1162 - 1169. 2006.
• Co-evolutionary Rates of Functionally Related Yeast Genes. Leonardo Marino-Ramirez, Olivier Bodenreider, Natalie Kantz and I. King Jordan. In Evolutionary Bioinformatics, Donald Forsdyke (ed), Springer (2006).
• The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. MAQC Consortium. Nature Biotechnology 24, 1151 - 1161. 2006.
• Using RNA sample titrations to assess microarray platform performance and normalization techniques. Shippy R et al. Nature Biotechnology 24, 1123-1131. 2006.
• Structure by design: from single proteins and their building blocks to nanostructures. Tsai C-J, Zheng J, Aleman C, Nussinov R. Trends in Biotechnoloy 24, 449-454. 2006 Oct.
• Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data.. Lusa L, McShane LM, Radmacher MD, Shih JH, Wright GW, Simon R. Stat Med. 2006 Jun.
• Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35. Zheng J, Ma B, Tsai C-J, Nussinov R. Biophysical Journal 91: 824-833. 2006.
• Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect Jang H, Ma B,Woolf TB. Biophysical Journal 91:2848-2859, 2006.
• Comparison of the Human and Worm p53 Structures Suggests a Way for Enhancing Stability. Pan Y, Ma B, Levine AJ, Nussinov R. Biochemistry, 45 (12), 3925 -3933, 2006.
• Titin as a giant scaffold for integrating stress and SH3-mediated signaling pathways: The clustering of novel overlap ligand motifs in the elastic PEVK segment. Ma K, Forbes JG, Gutierrez-Cruz G, and Wang K. J. Biol Chem. 2006 Jun; in print
• Structural and Molecular Interactions of CCR5 Inhibitors with CCR5. Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF, Arnold E, Mitsuya H. J Biol Chem. 281(18):12688-98. 2006 May.
• System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics. Mountain RD. J Chem Phys. 124(10):104109. 2006 Mar.

• The snail (Biomphalaria glabrata) genome project Raghavan N. and Knight M. Trends Parasitol. 22(4):148-51. (2006)
• The Stability of Monomeric Intermediates Controls Amyloid Formation: A{beta}25-35 and its N27Q Mutant.Ma B, Nussinov R. Biophys J. 2006 Feb.
• Altered HIV-1 Gag protein interactions with cyclophilin A (CypA) on the acquisition of H219Q and H219P substitutions in the CypA binding loop.Gatanaga H, Das D, Suzuki Y, Yeh DD, Hussain KA, Ghosh AK, Mitsuya H. J Biol Chem. 281(2):1241-50. 2006 Jan.

2005

• Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis. Klauda JB, Pastor RW, Brooks BR. J. Phys. Chem. B 109, 15684 -15686. 2005.
• Solution Structure of Enzyme IIAChitobiose from the N,N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System. Chun Tang, David C. Williams, Jr., Rodolfo Ghirlando, and G. Marius Clore. J. Biol. Chem, 280, Issue 12, 11770-11780. (2005).
• Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem. Sardiu ME, Alves G, Yu Y-K. Phys. Rev. E, 72, 061917 (2005)
• Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Alves G, Yu Y-K. Bioinformatics, 21(19), 3726-3732 (2005).
• Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1. Lopez de Silanes I, Galban S, Martindale JL, Yang X, Mazan-Mamczarz K, Indig FE, Falco G, Zhan M, Gorospe M. Mol. Cell. Biol., 25(21):9520-31 (2005).
• Sequential testing for efficacy in clinical trials with non-transient effects. James F. Troendle, Aiyi Liu, Chengqing Wu, Kai F. Yu. Statistics in Medicine, 24(21), 3239 - 3250 (2005).
• Quantification of brain phosphodiesterase 4 in rat with (R)-[11C]Rolipram-PET.. Fujita M, Zoghbi SS, Crescenzo MS, Hong J, Musachio JL, Lu JQ, Liow JS, Seneca N, Tipre DN, Cropley VL, Imaizumi M, Gee AD, Seidel J, Green MV, Pike VW, Innis RB. Neuroimage, 26(4):1201-10. (2005).
• Measurement of Ribose Carbon Chemical Shift Tensors for A-form RNA by Liquid Crystal NMR Spectroscopy. David L. Bryce, Alexander Grishaev, and Ad Bax. J. Am. Chem. Soc, 127 (20), 7387 -7396. (2005)
• PET imaging of brain with the beta-amyloid probe, [11C]6-OH-BTA-1, in a transgenic mouse model of Alzheimer's disease.. Toyama H, Ye D, Ichise M, Liow JS, Cai L, Jacobowitz D, Musachio JL, Hong J, Crescenzo M, Tipre D, Lu JQ, Zoghbi S, Vines DC, Seidel J, Katada K, Green MV, Pike VW, Cohen RM, Innis RB. Eur. J. Nucl. Med. Mol. Imaging, 32(5):593-600. (2005).
• Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids. Lague P, Roux B, Pastor RW. J. Mol. Biol 354, 1129-1141. 2005.
• A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose. Skibinsky A, Venable RM, Pastor RW. Biophys J 89 4111-4121. 2005.
• Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations. Christine Peter and Gerhard Hummer. Biophys. J, 89:2222-2234 (2005).
• An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer. Klauda J, Brooks BR, MacKerell AD, Venable RM, Pastor RW. J. Phys. Chem. B 109 (11), 5300 -5311. 2005.
• Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference. Costanzi S, Joshi BV, Maddileti S, Mamedova L, Gonzalez-Moa MJ, Marquez VE, Harden TK, Jacobson KA. J Med Chem. 48(26):8108-11. 2005 Dec.
• Computed tomographic virtual colonoscopy computer-aided polyp detection in a screening population. Summers RM, Yao J, Pickhardt PJ, Franaszek M, Bitter I, Brickman D, Krishna V, Choi JR. Gastroenterology. 129(6):1832-44. 2005 Dec.
• Progress in refining virtual colonoscopy for colorectal cancer screening. Bond JH. Gastroenterology. 129(6):1832-44. 2005 Dec.
• Molecular Dynamics Simulations of Alzheimer's beta-Amyloid Protofilaments Buchete NV, Tycko R, and Hummer G. Mol. Biol. 353 (4): 804-821. 2005 Nov.
• Modelling longitudinal semicontinuous emesis volume data with serial correlation in an acupuncture clinical trial Albert, P.S. and Shen J. J. Roy. Statist. Soc. Ser. C., 54:707-720. 2005 Aug.
• CD4 binding partially locks the bridging sheet in gp120 but leaves the beta2/3 strands flexible.Pan Y, Ma B, Nussinov R. J Mol Biol. 350(3):514-27. 2005 Jul.
• Genome-wide assembly and analysis of alternative transcripts in mouse. Sharov AA, Dudekula DB, Ko MSH. Genome Res. 15:748-754. 2005.
• Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction. Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR. Chem. & Biodivers. 2:447-456. 2005

• Molecular architecture of a eukaryotic DNA transposase. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F. Nat Struct Mol Biol. 2005 Jul
• Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. Proc Natl Acad Sci U S A. 102(23):8174-9. 2005 Jun.
• Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface. Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. Proc Natl Acad Sci U S A. 102(11):3988-93. 2005 Mar.
• Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties. Li X, Hassan SA, Mehler EL. Proteins. 2005 Jun.

• Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Cam H, Sugiyama T, Chen ES, Chen X, Fitzgerald P, Grewal SI. Nat Genet. 2005 Jun.
• From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations. SA Hassan, EL Mehler. Int.Quantum Chem. 2005 Apr.
• Comparison of the protein/protein interfaces in the p53 VDNA crystal structures: Towards elucidation of the biological interface. Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. Proc Natl Acad Sci U S A. 102(11):3988-93.
• In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1. Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R. Biochemistry. 44(5):1423-32. 2005 Feb.
• Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. Proc Natl Acad Sci U S A. 102(8):2754-9. 2005 Feb.
• Agonist-Induced Conformational Changes in Thyrotropin-Releasing Hormone Receptor Type I: Disulfide Cross-Linking and Molecular Modeling Approaches. Huang W, Osman R, Gershengorn MC. Biochemistry. 44(7):2419-2431. 2005 Feb.

• A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core. Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. J Mol Biol. 345(5):1213-27. 2005 Feb.

2004

• Three Roads to Islet Bursting: Emergent Oscillations in Coupled Phantom Bursters. Charles L. Zimliki, David Mears and Arthur Sherman. Biophys. J, 87:193-206 (2004).
• Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Robert J Clifford, Michael N Edmonson, Cu Nguyen, Kenneth J Buetow. Bioinformatics, 20(7), 1006-1014 (2004).
• Evaluation of anesthesia effects on [18F]FDG uptake in mouse brain and heart using small animal PET.. Toyama H, Ichise M, Liow JS, Vines DC, Seneca NM, Modell KJ, Seidel J, Green MV, Innis RB. Nucl. Med. Biol., 31(2):251-6. (2004).
• Impact of Azaproline on Peptide Conformation. Ye Che and Garland Marshall. J. Org. Chem, 69 (26), 9030 -9042 (2004).
• Absolute quantification of regional cerebral glucose utilization in mice by 18F-FDG small animal PET scanning and 2-14C-DG autoradiography.. Toyama H, Ichise M, Liow JS, Modell KJ, Vines DC, Esaki T, Cook M, Seidel J, Sokoloff L, Green MV, Innis RB. J. Nucl. Med, 45(8):1398-405. (2004).
• An Example of Slow Convergence of the Bootstrap in High Dimensions. Troendle J.F.; Korn E.L.; McShane L.M. The American Statistician, 58(1), 25-29 (2004).
• In silico protein design by combinatorial assembly of protein building blocks. Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Buyong Ma and Ruth Nussinov. Protein Science, 13:2753-2765 (2004).
• Synthesis and evaluation of two 18F-labeled 6-iodo-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridine derivatives as prospective radioligands for beta-amyloid in Alzheimer's disease.. Cai L, Chin FT, Pike VW, Toyama H, Liow JS, Zoghbi SS, Modell K, Briard E, Shetty HU, Sinclair K, Donohue S, Tipre D, Kung MP, Dagostin C, Widdowson DA, Green M, Gao W, Herman MM, Ichise M, Innis RB. J. Med. Chem, 47(9):2208-18 (2004).
• Nucleic acid transport through carbon nanotube membranes. In-Chul Yeh and Gerhard Hummer. PNAS< 101(33): 12177-12182 (2004).
• Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function. Goonesekere NC, Lee B. Nucleic Acids Res, 32(9):2838-43. (2004).
• Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces. Patrick Lague, Richard W. Pastor, Bernard R Brooks. J. Phys. Chem. B, 108, 363-368 (2004).
• Mapping Development-Related and Age-Related Chromatin Remodeling by a High Throughput ChIP-HPLC Approach. Valya R. Russanova, Tazuko H. Hirai, Andrei V. Tchernov and Bruce H. Howard J. Gerontology, 59:1234-1243 (2004).
• Visualization of alpha-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase. Borgnia MJ, Shi D, Zhang P, Milne JL J. Struct. Biol., 147(2):136-45. (2004).
• Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations. In-Chul Yeh and Gerhard Hummer. Biophys. J, 86:681-689 (2004)
• Combinatorial modeling of protein folding kinetics: free energy profiles and rates. Eric R. Henry and William A. Eaton Chemical Physics, 307, 163-185 (2004).
• An efficient algorithm for generating two-way contingency tables with fixed marginal totals and arbitrary mean proportions, with applications to permutation tests. Craig Borkowf. Comp. Stat. and Data Analysis, 44(3), 431-449 (2004).
• Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design. Karki RG, Tang Y, Burke TR Jr, Nicklaus MC. J Comput Aided Mol Des. 18(12):739-60. 2004 Dec.
• Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling. Valya R. Russanova, Tazuko H. Hirai and Bruce H. Howard J. Gerontology, 59:1221-1233 (2004)
• Performance of a genetic algorithm for mass spectrometry proteomics. Jeffries, NO. BMC Bioinformatics, 5:180 (2004).
• Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation. Daron I. Freedberg, Richard M. Venable, Angelo Rossi, Thomas E. Bull, and Richard W. Pastor. J. Am. Chem. Soc, 126, 10478-10484 (2004).
• Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium Hassan SA J. Phys. Chem. B. 108 (50):19501-19509. 2004.
• Correcting log ratios for signal saturation in cDNA microarrays. Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Bioinformatics. 20(16):2685-93. 2004 Nov.
• Identifying multiple changepoints in heterogeneous binary data with an application to molecular genetics. Albert PS, Hunsberger SA, Hu N, Taylor PR. Biostatistics. 5(4):515-529. 2004 Oct.
• Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. Ma B, Nussinov R. J Biol Chem. 279(51):53875-85.
• Insights into amyloid structural formation and assembly through computational approaches. Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R. Amyloid. 11(3):143-61. 2004 Sep.
• Controlling the number of false discoveries: application to high-dimensional genomic data Korn EL, Troendle JF, McShane LMLM, and Simon R. Journal of Statistical Planning and Inference. 124(2)379-398. 2004 Sep.

• Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Templeton TJ, Iyer LM, Anantharaman V, Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L. Genome Res. 14(9):1686-95. 2004 Sep.
• Clustering of DNA sequences in human promoters. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Genome Res. 14(8):1562-74. 2004 Aug.
• Reversible proton transfer dynamics in bacteriorhodopsin Lee YS and Krauss M. J. Mol. Stru. 700(3):243-246. 2004 Aug.
• A Model of Inverse Agonist Action at Thyrotropin-Releasing Hormone Receptor Type 1: Role of a Conserved Tryptophan in Helix 6. Lu X, Huang W, Worthington S, Drabik P, Osman R, Gershengorn MC. Mol Pharmacol. 66(5):1192-200. 2004 Aug.
• Exploring peptide energy landscapes: A test of force fields and implicit solvent models. Steinbach PJ. Proteins. 57(4):665-677. 2004 Aug.
• Quantum chemical calculations and mutational analysis suggest heat shock protein 90 catalyzes trans-cis isomerization of geldanamycin. Lee YS, Marcu MG, Neckers L. Chem Biol. 11(7):991-8. 2004 Jul.
• A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard. Albert PS, Dodd LE. Biometrics. 60(2):427-35. 2004 Jun.
• Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain. Pan Y, Ma B, Keskin O, Nussinov R. J Biol Chem. 16;279(29):30523-30. 2004 Jul.
• The stability and dynamics of the human calcitonin amyloid peptide DFNKF. Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. Biophys J. 87(1):146-58. 2004 Jul.

• Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3. Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H. J Biol Chem. 279(23):24624-30. 2004 Jun.
• Beta-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water. Wu X and Bernard R. Brooks. Biophys J. 86(4):1946-58. 2004 Apr.
• Peptide sequence and amyloid formation; molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs. Zanuy D, Porat Y, Gazit E, Nussinov R. Structure (Camb). 12(3):439-55. 2004 Mar.
• Evolutionary and functional relationships within the DJ1 superfamily. Bandyopadhyay S, Cookson MR. BMC Evol Biol. 4(1):6. 2004 Feb.
• Dynamics of proton transfer in bacteriorhodopsin. Lee YS, Krauss M. J Am Chem Soc. 126(7):2225-30. 2004 Feb.
• Statistical analysis of over-represented words in human promoter sequences. Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Nucleic Acids Res. 32(3):949-58. 2004 Feb.
• Large scale validation of a computer aided polyp detection algorithm for CT colonography using cluster computing. I Bitter, JE Brown, D Brickman, RM Summers. 2004.

More Publications

Research projects (2005 and earlier)